Analysis of intact glycopeptides by mass spectrometry is essential to determining the microheterogeneity of protein glycosylation. Higher-energy collisional dissociation (HCD) fragmentation of glycopeptides generates mono- or disaccharide ions called oxonium ions that carry information about the structure of the fragmented glycans. Here, we investigated the link between glycan structures and th...

The centrally important role of acids in aqueous chemistry has stimulated the search for the smallest droplet of hydrochloric acid. Based on several independent quantum calculations, this appears to be the HCl(H2O)4 cluster, which dissociates into the so-called solvent ion pair (SIP), H3O(+)(H2O)3Cl(-). Experimental verification of this prediction via infra-red spectroscopy is a major challenge...

We report on a new approach for studying fragmentation channels in Proton Transfer Reaction-Mass Spectrometry (PTR-MS), which we name primary ion depletion kinetics (PIDK). PTR-MS is a chemical ionization mass spectrometric (CIMS) technique deploying hydronium ions for the chemical ionization. Induced by extremely high concentrations of analyte M, depletion of the primary ions in the drift tube...

Purification and liquid chromatography-tandem mass spectrometry (LC-MS/MS) characterization of glycopeptides, originating from protease digests of glycoproteins, enables site-specific analysis of protein N- and O-glycosylations. We have described a protocol to enrich, hydrolyze by chondroitinase ABC, and characterize chondroitin sulfate-containing glycopeptides (CS-glycopeptides) using positive...

Synthetic, polycrystalline samples of alunite [K0.88(H3O)0.12Al2.64(SO4)2(OH)4.92(H2O)1.08] and oxonium-substituted alunite [H3OAl2.87(SO4)2(OH)5.61(H2O)0.39] have been investigated using incoherent, inelastic neutron-scattering (IINS) methods in order to determine the nature of the non-OH “H2O”. IINS measurements were made on non-deuterated samples at 20 K using the HRMECS chopper spectrometer...

Site-specific characterization of glycoform heterogeneity currently requires glycan structure assignment and glycopeptide quantification in two independent experiments. We present here a new method combining multiple reaction monitoring mass spectrometry with energy-resolved structural analysis, which we termed "energy-resolved oxonium ion monitoring". We demonstrated that monitoring the yields...

The 2-tert-butyl-3-phenylphosphirenylium ion 13 is formed in abundance in the gas phase from 1-chloro-1H-phosphirene 6 upon 70 eV electron ionization. Collision-induced dissociation (CID) and ion-molecule reactions followed by CID of the product ions were performed via pentaquadrupole mass spectrometry to probe the structure and reactivity of 13 towards representative nucleophiles and dienes. U...

A sequential Diels-Alder reaction/silicon-directed [4 + 2]-annulation was developed to assemble hydroisochromene-type ring systems from menadione 2. In the first step, a Diels-Alder of the 1-silyl-substituted butadiene 1 with 2 furnished an intermediate cyclic allylsilane. Subsequently, TMSOTf promoted a [4 + 2]-annulation through trapping of an oxonium, generated by condensation between an ald...